General Biology Study Notes: Pigments, Vision, Evolution, and Proteins

Unit 2 & 3: Life & Evolution

Role of Pigments in Vision

Pigment molecules play a crucial role in vision by absorbing light energy, enabling the conversion of light into biological signals. These molecules have distinct molecular structures but share the ability to interact with photons.

• Pigments are molecules that absorb specific wavelengths of light due to their molecular structure.

• Despite structural differences, all pigments contain conjugated double bonds that allow them to absorb light.

• Example: Retinal in photoreceptor cells is a pigment that changes shape when it absorbs light, initiating the visual process.

Light as a Source of Information

Light provides essential information for organisms, especially in vision. The retina is a layered structure containing specialized cells that detect and process light.

• Cells in the retina are organized in layers, with photoreceptors (rods and cones) located in the outermost layer.

• Rods detect low light and are responsible for night vision; cones detect color and function in bright light.

• Photoreceptors contain pigments that absorb photons and trigger a signal transduction cascade.

• Upon photon absorption, a conformational change occurs in the pigment molecule, leading to electrical signals sent to the brain.

• Example: The absorption of a photon by retinal in rhodopsin causes it to change from the 11-cis to the all-trans form.

Colour (Chromatic) Vision: Cone Cells

Cone cells in the retina enable the perception of color by responding to different wavelengths of light. This process allows the brain to interpret color information from the environment.

• Three types of cone cells: Short Wave Sensitive (SWS), Medium Wave Sensitive (MWS), and Long Wave Sensitive (LWS).

• Each type contains a different opsin protein, which determines its wavelength sensitivity.

• Individuals with all three opsins have trichromatic vision; those with only two have dichromatic vision.

• Example: Humans typically have trichromatic vision, while some mammals have dichromatic vision.

Opsin Type	Wavelength Sensitivity
Short Wave Sensitive (SWS)	Blue
Medium Wave Sensitive (MWS)	Green
Long Wave Sensitive (LWS)	Red

Fundamental Characteristics of Life in All Organisms

All living organisms share several fundamental characteristics that define life and its processes.

• Composed of cells

• Capable of replication

• Undergo evolution

• Process information

• Require energy

Theory of Evolution by Natural Selection

Evolution by natural selection is a unifying concept in biology, explaining both the unity and diversity of life. All organisms alive today descended from a common ancestor.

• Populations change over time due to natural selection.

• Individuals with heritable traits that confer advantages are more likely to survive and reproduce.

• Phylogenetic trees illustrate evolutionary relationships and the unity/diversity of life.

• Example: The branching pattern of a phylogenetic tree shows how species diverged from common ancestors.

Genetics of Color Vision

The ability to perceive color is determined by genes encoding opsin proteins in photoreceptor cells. These genes are located on chromosomes and follow the central dogma of molecular biology.

• A gene encodes an opsin protein, which forms part of a photoreceptor unit in a cell.

• Central dogma: DNA → RNA → Protein

• Functional units (photoreceptors) allow organisms to detect and interpret light.

• Example: Mutations in opsin genes can lead to color blindness.

Key Points about Selection

Natural selection drives evolution by favoring individuals that are best adapted to their environment.

• Survival and reproduction are key to passing genes to the next generation.

• Populations evolve, not individuals.

• Selection is influenced by environmental circumstances, which can change over time.

• Example: Peppered moths changed color in response to industrial pollution, demonstrating selection in action.

Unity of Life: Shared Characteristics Across Domains

Cells in all three domains of life—Bacteria, Archaea, and Eukarya—share fundamental characteristics that reflect their common ancestry.

• Basic building blocks (biomolecules)

• Genetic information flow: $\text{DNA} \rightarrow \text{RNA} \rightarrow \text{Protein}$

• Plasma membrane

• Energy metabolism

Domain	Shared Characteristics
Bacteria	Basic biomolecules, genetic flow, plasma membrane, energy metabolism
Archaea	Basic biomolecules, genetic flow, plasma membrane, energy metabolism
Eukarya	Basic biomolecules, genetic flow, plasma membrane, energy metabolism

Proteins and Their Functions

Protein Structure and Function

Proteins are essential biomolecules that carry out many of life's critical functions. Their structure determines their function.

• Proteins are polymers of amino acids linked by peptide bonds.

• Each amino acid has a unique side chain (R group) that determines its chemical and physical properties.

• The primary structure of a protein is its unique sequence of amino acids.

• Example: Collagen is a structural protein found in connective tissues.

Protein Level	Description
Primary	Sequence of amino acids
Secondary	Alpha helices and beta sheets formed by hydrogen bonding
Tertiary	Three-dimensional folding due to side chain interactions
Quaternary	Assembly of multiple polypeptide chains

• Peptide bond formation:

$\text{Amino Acid}_1 + \text{Amino Acid}_2 \rightarrow \text{Dipeptide} + \text{H}_2\text{O}$

• Central Dogma of Molecular Biology:

$\text{DNA} \rightarrow \text{RNA} \rightarrow \text{Protein}$

Additional info: Some explanations and examples have been expanded for clarity and completeness.